------------------------------------------------------------ Pratt version 2.1, Sept. 1996 Written by Inge Jonassen, University of Bergen Norway email: inge@ii.uib.no For more information, see http://www.ii.uib.no/~inge/Pratt.html ------------------------------------------------------------ Please quote: I.Jonassen, J.F.Collins, D.G.Higgins. Protein Science 1995;4(8):1587-1595. ------------------------------------------------------------ Pratt version 2.1 Analysing 5 sequences from file COBALAMIN_BINDING PATTERN CONSERVATION: CM: min Nr of Seqs to Match 5 C%: min Percentage Seqs to Match 100.0 PATTERN RESTRICTIONS : PP: pos in seq [off,complete,start] off PL: max Pattern Length 50 PN: max Nr of Pattern Symbols 50 PX: max Nr of consecutive x's 5 FN: max Nr of flexible spacers 2 FL: max Flexibility 2 FP: max Flex.Product 10 BI: Input Pattern Symbol File off BN: Nr of Pattern Symbols Initial Search 20 PATTERN SCORING: S: Scoring [info,mdl,tree,dist,ppv] info SEARCH PARAMETERS: G: Pattern Graph from [seq,al,query] seq E: Search Greediness 3 R: Pattern Refinement on RG: Generalise ambiguous symbols off OUTPUT: OF: Output Filename COBALAMIN_BINDING.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HAPC_PIG 416 IF_HUMAN 417 IF_RAT 421 TCO1_HUMAN 433 TCO2_HUMAN 427 Pratt run started at Thu Feb 6 19:08:35 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 37.5305 5( 5) V-D-T-x-A-x-A-x-L-A-x-T-C 2: 33.3604 5( 5) D-T-x-A-x-A-x-L-A-x-T-C 3: 29.1904 5( 5) Q-x-L-P-x-L-x(2)-K-T-x(2)-D 4: 29.1904 5( 5) T-x-A-x-A-x-L-A-x-T-C 5: 28.1904 5( 5) Q-x-L-P-x-L-x(2)-K-T-x(1,3)-L 6: 25.0203 5( 5) A-x-A-x-L-A-x-T-C 7: 24.5203 6( 5) L-x(0,1)-P-x-L-x(2)-K-T-x(2)-D 8: 24.5203 5( 5) S-x(2)-T-x(3)-A-x(2,3)-A-x-T-x(4)-S 9: 24.0203 5( 5) L-P-x-L-x(2)-K-T-x(1,3)-L 10: 23.0203 6( 5) G-x(0,2)-A-x(3)-L-A-L-x(1,3)-C 11: 20.8503 5( 5) P-x-L-x(2)-K-T-x(2)-D 12: 20.3503 5( 5) A-x(0,1)-L-A-x-T-C 13: 20.3503 5( 5) Q-L-x(2)-V-x(0,1)-L-x(5)-I 14: 19.8503 5( 5) P-x-L-x(2)-K-T-x(1,3)-L 15: 19.8503 5( 5) P-x(1,2)-L-x(1,2)-K-T-x(2)-D 16: 19.8503 5( 5) A-x(3)-P-x(2,3)-G-x-T-x(1,2)-L 17: 19.8503 5( 5) F-x(4)-G-x(2,3)-A-x(0,1)-L-x(3)-C 18: 19.8503 5( 5) L-x-I-L-A-x(1,3)-C 19: 19.3503 6( 5) L-x(0,2)-L-x(1,2)-K-T-x(2)-D 20: 19.3503 5( 5) P-x(3)-A-x(1,2)-L-x(2,4)-L-x(5)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 52.8924 5( 5) V-D-T-[AG]-A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] B 2: 48.7224 5( 5) D-T-[AG]-A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] C 3: 48.4723 5( 5) P-x-[APS]-[AGI]-A-x(1,2)-L-x(2,4)-L-x-[AG]-[KR]-[TV]-x-L-x-[AIV]-[NPST]-x(4)-[ACGSV]-x(3)-[AEQS]-[GLV]-x(2)-[NST] D 4: 44.5523 5( 5) T-[AG]-A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] E 5: 40.9204 5( 5) Q-x-L-P-[ASV]-L-x(2)-K-T-[FY]-[IL]-D-[ILV] F 6: 40.8645 5( 5) S-x(2)-T-[AGL]-[AP]-[IMV]-A-x(2,3)-A-x-T-x-[LMV]-x(2)-S-x(3)-[GNPS]-x(3)-[AGQ] G 7: 38.6841 5( 5) Q-[ILV]-L-P-[ASV]-L-x(2)-K-T-x(1,3)-L-x-[FIV]-[NPT] H 8: 37.2122 5( 5) A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] I 9: 34.9818 5( 5) F-x-[FV]-x(2)-G-x(2,3)-A-x(0,1)-L-[AT]-x(2)-C-x(4)-[ILM]-x-[NSV]-x(3)-[EK] J 10: 34.9346 5( 5) G-x(0,2)-A-[LMV]-x(2)-L-A-L-x(1,3)-C-x(4)-[GIL]-x(2)-G-x(3)-[AGNV] K 11: 33.6533 6( 5) L-x(0,1)-P-x-L-x(2)-K-T-[FY]-[IL]-D-[ILV] L 12: 32.6238 5( 5) Q-L-x-[GLP]-V-x(0,1)-L-x(5)-I-[DENP]-x(2)-[FLV]-x-[DEQS]-x(3)-[LPV] M 13: 32.0743 5( 5) A-[DQ]-x(2)-P-x(2,3)-G-[EK]-T-x(1,2)-L-[DR]-[ILV] N 14: 31.8522 5( 5) L-P-[ASV]-L-x(2)-K-T-x(1,3)-L-x-[FIV]-[NPT] O 15: 29.9832 5( 5) P-x-L-x(2)-K-T-[FY]-[IL]-D-[ILV] P 16: 28.9832 5( 5) P-x(1,2)-L-x(1,2)-K-T-[FY]-[IL]-D-[ILV] Q 17: 28.4832 6( 5) L-x(0,2)-L-x(1,2)-K-T-[FY]-[IL]-D-[ILV] R 18: 26.4555 5( 5) A-x(0,1)-L-A-[FL]-T-C-[LMV] S 19: 25.0850 5( 5) P-x-L-x(2)-K-T-x(1,3)-L-x-[FIV]-[NPT] T 20: 22.5282 5( 5) L-[AGI]-I-L-A-x(1,3)-C Best patterns with alignements: fitness hits(seqs) Pattern A 1: 52.8924 5( 5) V-D-T-[AG]-A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] Occurences: 5(5) HAPC_PIG : 185- 198: sghfs VDTGAVAVLALTCV krsis IF_HUMAN : 170- 183: sspfn VDTGAMATLALTCM ynkip IF_RAT : 174- 187: sspfs VDTGAVATLALTCM ynrip TCO1_HUMAN : 185- 198: gsqfs VDTGAMAVLALTCV kksli TCO2_HUMAN : 193- 206: qghhs VDTAAMAGLAFTCL krsnf B 2: 48.7224 5( 5) D-T-[AG]-A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] Occurences: 5(5) HAPC_PIG : 186- 198: ghfsv DTGAVAVLALTCV krsis IF_HUMAN : 171- 183: spfnv DTGAMATLALTCM ynkip IF_RAT : 175- 187: spfsv DTGAVATLALTCM ynrip TCO1_HUMAN : 186- 198: sqfsv DTGAMAVLALTCV kksli TCO2_HUMAN : 194- 206: ghhsv DTAAMAGLAFTCL krsnf C 3: 48.4723 5( 5) P-x-[APS]-[AGI]-A-x(1,2)-L-x(2,4)-L-x-[AG]-[KR]-[TV]-x-L-x-[AIV]-[NPST]-x(4)-[ACGSV]-x(3)-[AEQS]-[GLV]-x(2)-[NST] Occurences: 5(5) HAPC_PIG : 281- 313: gvfrl PiAAAqiLpa--LlGKTyLdVTklllVpkvQVniT depvp IF_HUMAN : 265- 297: gkfhn PmSIAqiLps--LkGKTyLdVPqvtcSpdhEVqpT lpsnp IF_RAT : 269- 301: gkfqn PmSIAqiLps--LkGKTyLdVPqvtcGpdhEVppT ltdyp TCO1_HUMAN : 284- 316: gafsn PnAAAqvLpa--LmGKTfLdINkdssCvsaSGnfN isade TCO2_HUMAN : 257- 290: flmts PmPGAe-LgtacLkARVaLlASlqdgAfqnALmiS qllpv D 4: 44.5523 5( 5) T-[AG]-A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] Occurences: 5(5) HAPC_PIG : 187- 198: hfsvd TGAVAVLALTCV krsis IF_HUMAN : 172- 183: pfnvd TGAMATLALTCM ynkip IF_RAT : 176- 187: pfsvd TGAVATLALTCM ynrip TCO1_HUMAN : 187- 198: qfsvd TGAMAVLALTCV kksli TCO2_HUMAN : 195- 206: hhsvd TAAMAGLAFTCL krsnf E 5: 40.9204 5( 5) Q-x-L-P-[ASV]-L-x(2)-K-T-[FY]-[IL]-D-[ILV] Occurences: 5(5) HAPC_PIG : 286- 299: piaaa QiLPALlgKTYLDV tklll IF_HUMAN : 270- 283: pmsia QiLPSLkgKTYLDV pqvtc IF_RAT : 274- 287: pmsia QiLPSLkgKTYLDV pqvtc TCO1_HUMAN : 289- 302: pnaaa QvLPALmgKTFLDI nkdss TCO2_HUMAN : 291- 304: almis QlLPVLnhKTYIDL ifpdc F 6: 40.8645 5( 5) S-x(2)-T-[AGL]-[AP]-[IMV]-A-x(2,3)-A-x-T-x-[LMV]-x(2)-S-x(3)-[GNPS]-x(3)-[AGQ] Occurences: 5(5) HAPC_PIG : 184- 209: lsghf SvdTGAVAvl-AlTcVkrSisnGkikA aikds IF_HUMAN : 147- 173: lcqkn SeaTLPIAvrfAkTlLanSspfNvdtG amatl IF_RAT : 151- 177: lcqkn SeaTLPIAvrfAkTlMmeSspfSvdtG avatl TCO1_HUMAN : 184- 209: fgsqf SvdTGAMAvl-AlTcVkkSlinGqikA degsl TCO2_HUMAN : 192- 217: hqghh SvdTAAMAgl-AfTcLkrSnfnPgrrQ ritma G 7: 38.6841 5( 5) Q-[ILV]-L-P-[ASV]-L-x(2)-K-T-x(1,3)-L-x-[FIV]-[NPT] Occurences: 5(5) HAPC_PIG : 286- 300: piaaa QILPALlgKTy--LdVT klllv IF_HUMAN : 270- 284: pmsia QILPSLkgKTy--LdVP qvtcs IF_RAT : 274- 288: pmsia QILPSLkgKTy--LdVP qvtcg TCO1_HUMAN : 289- 303: pnaaa QVLPALmgKTf--LdIN kdssc TCO2_HUMAN : 291- 307: almis QLLPVLnhKTyidLiFP dclap H 8: 37.2122 5( 5) A-[MV]-A-[GTV]-L-A-[FL]-T-C-[LMV] Occurences: 5(5) HAPC_PIG : 189- 198: svdtg AVAVLALTCV krsis IF_HUMAN : 174- 183: nvdtg AMATLALTCM ynkip IF_RAT : 178- 187: svdtg AVATLALTCM ynrip TCO1_HUMAN : 189- 198: svdtg AMAVLALTCV kksli TCO2_HUMAN : 197- 206: svdta AMAGLAFTCL krsnf I 9: 34.9818 5( 5) F-x-[FV]-x(2)-G-x(2,3)-A-x(0,1)-L-[AT]-x(2)-C-x(4)-[ILM]-x-[NSV]-x(3)-[EK] Occurences: 5(5) HAPC_PIG : 183- 208: nlsgh FsVdtGav-AvLAltCvkrsIsNgkiK aaikd IF_HUMAN : 168- 193: anssp FnVdtGam-AtLAltCmynkIpVgseE gyrsl IF_RAT : 172- 197: messp FsVdtGav-AtLAltCmynrIpVgsqE nyrdl TCO1_HUMAN : 183- 208: yfgsq FsVdtGam-AvLAltCvkksLiNgqiK adegs TCO2_HUMAN : 7- 32: rhlga FlFllGvlgA-LTemCeipeMdShlvE klgqh J 10: 34.9346 5( 5) G-x(0,2)-A-[LMV]-x(2)-L-A-L-x(1,3)-C-x(4)-[GIL]-x(2)-G-x(3)-[AGNV] Occurences: 5(5) HAPC_PIG : 188- 209: fsvdt G--AVavLALt--CvkrsIsnGkikA aikds IF_HUMAN : 173- 194: fnvdt G--AMatLALt--CmynkIpvGseeG yrslf IF_RAT : 177- 198: fsvdt G--AVatLALt--CmynrIpvGsqeN yrdlf TCO1_HUMAN : 188- 209: fsvdt G--AMavLALt--CvkksLinGqikA degsl TCO2_HUMAN : 103- 128: gkpsm GqlALylLALranCefvrGhkGdrlV sqlkw K 11: 33.6533 6( 5) L-x(0,1)-P-x-L-x(2)-K-T-[FY]-[IL]-D-[ILV] Occurences: 6(5) HAPC_PIG : 288- 299: aaaqi L-PaLlgKTYLDV tklll IF_HUMAN : 272- 283: siaqi L-PsLkgKTYLDV pqvtc IF_RAT : 276- 287: siaqi L-PsLkgKTYLDV pqvtc TCO1_HUMAN : 291- 302: aaaqv L-PaLmgKTFLDI nkdss TCO2_HUMAN : 292- 304: lmisq LlPvLnhKTYIDL ifpdc TCO2_HUMAN : 293- 304: misql L-PvLnhKTYIDL ifpdc L 12: 32.6238 5( 5) Q-L-x-[GLP]-V-x(0,1)-L-x(5)-I-[DENP]-x(2)-[FLV]-x-[DEQS]-x(3)-[LPV] Occurences: 5(5) HAPC_PIG : 5- 27: rqsh QLpLVgLllfslIPsqLcQscvV sekdy IF_HUMAN : 321- 343: ytinn QLrGVeLlfnetINvsVkSgsvL lvvle IF_RAT : 325- 347: ytinn QLrGVdLlfnvtIEvsVkSgsvL lavle TCO1_HUMAN : 6- 28: mrqsh QLpLVgLllfsfIPsqLcEiceV seeny TCO2_HUMAN : 291- 312: almis QLlPV-LnhktyIDliFpDclaP rvmle M 13: 32.0743 5( 5) A-[DQ]-x(2)-P-x(2,3)-G-[EK]-T-x(1,2)-L-[DR]-[ILV] Occurences: 5(5) HAPC_PIG : 285- 299: lpiaa AQilPallGKTy-LDV tklll IF_HUMAN : 269- 283: npmsi AQilPslkGKTy-LDV pqvtc IF_RAT : 273- 287: npmsi AQilPslkGKTy-LDV pqvtc TCO1_HUMAN : 288- 302: npnaa AQvlPalmGKTf-LDI nkdss TCO2_HUMAN : 410- 424: llqgi ADyrPkd-GETieLRL vsw N 14: 31.8522 5( 5) L-P-[ASV]-L-x(2)-K-T-x(1,3)-L-x-[FIV]-[NPT] Occurences: 5(5) HAPC_PIG : 288- 300: aaaqi LPALlgKTy--LdVT klllv IF_HUMAN : 272- 284: siaqi LPSLkgKTy--LdVP qvtcs IF_RAT : 276- 288: siaqi LPSLkgKTy--LdVP qvtcg TCO1_HUMAN : 291- 303: aaaqv LPALmgKTf--LdIN kdssc TCO2_HUMAN : 293- 307: misql LPVLnhKTyidLiFP dclap O 15: 29.9832 5( 5) P-x-L-x(2)-K-T-[FY]-[IL]-D-[ILV] Occurences: 5(5) HAPC_PIG : 289- 299: aaqil PaLlgKTYLDV tklll IF_HUMAN : 273- 283: iaqil PsLkgKTYLDV pqvtc IF_RAT : 277- 287: iaqil PsLkgKTYLDV pqvtc TCO1_HUMAN : 292- 302: aaqvl PaLmgKTFLDI nkdss TCO2_HUMAN : 294- 304: isqll PvLnhKTYIDL ifpdc P 16: 28.9832 5( 5) P-x(1,2)-L-x(1,2)-K-T-[FY]-[IL]-D-[ILV] Occurences: 5(5) HAPC_PIG : 289- 299: aaqil PalLg-KTYLDV tklll HAPC_PIG : 289- 299: aaqil Pa-LlgKTYLDV tklll IF_HUMAN : 273- 283: iaqil Ps-LkgKTYLDV pqvtc IF_RAT : 277- 287: iaqil Ps-LkgKTYLDV pqvtc TCO1_HUMAN : 292- 302: aaqvl Pa-LmgKTFLDI nkdss TCO2_HUMAN : 294- 304: isqll Pv-LnhKTYIDL ifpdc Q 17: 28.4832 6( 5) L-x(0,2)-L-x(1,2)-K-T-[FY]-[IL]-D-[ILV] Occurences: 6(5) HAPC_PIG : 288- 299: aaaqi LpaLlgKTYLDV tklll HAPC_PIG : 291- 299: qilpa L--Lg-KTYLDV tklll IF_HUMAN : 272- 283: siaqi LpsLkgKTYLDV pqvtc IF_RAT : 276- 287: siaqi LpsLkgKTYLDV pqvtc TCO1_HUMAN : 291- 302: aaaqv LpaLmgKTFLDI nkdss TCO2_HUMAN : 293- 304: misql LpvLnhKTYIDL ifpdc R 18: 26.4555 5( 5) A-x(0,1)-L-A-[FL]-T-C-[LMV] Occurences: 5(5) HAPC_PIG : 191- 198: dtgav AvLALTCV krsis IF_HUMAN : 176- 183: dtgam AtLALTCM ynkip IF_RAT : 180- 187: dtgav AtLALTCM ynrip TCO1_HUMAN : 191- 198: dtgam AvLALTCV kksli TCO2_HUMAN : 199- 206: dtaam AgLAFTCL krsnf S 19: 25.0850 5( 5) P-x-L-x(2)-K-T-x(1,3)-L-x-[FIV]-[NPT] Occurences: 5(5) HAPC_PIG : 289- 300: aaqil PaLlgKTy--LdVT klllv IF_HUMAN : 273- 284: iaqil PsLkgKTy--LdVP qvtcs IF_RAT : 277- 288: iaqil PsLkgKTy--LdVP qvtcg TCO1_HUMAN : 292- 303: aaqvl PaLmgKTf--LdIN kdssc TCO2_HUMAN : 294- 307: isqll PvLnhKTyidLiFP dclap T 20: 22.5282 5( 5) L-[AGI]-I-L-A-x(1,3)-C Occurences: 5(5) HAPC_PIG : 97- 105: sgqla LIILAfgaC ktpdv IF_HUMAN : 137- 143: fygps LAILAl--C qknse IF_RAT : 141- 147: fygpa LAILAl--C qknse TCO1_HUMAN : 97- 105: sgela LIILAlgvC rnaee TCO2_HUMAN : 159- 165: yyqyg LGILAl--C lhqkr Number of patterns evaluated by Pratt:13454 Total running time: 5 seconds